nf-core_modules/modules/bcftools/mpileup/main.nf
Harshil Patel 682f789f93
Bump tool versions for modules required in viralrecon (#1859)
* Bump tool versions for modules required in viralrecon

* Fix all the tests

* Fix Prettier lint

* Remove empty md5sums
2022-07-07 14:48:04 +01:00

53 lines
1.7 KiB
Text

process BCFTOOLS_MPILEUP {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0':
'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }"
input:
tuple val(meta), path(bam)
path fasta
val save_mpileup
output:
tuple val(meta), path("*.gz") , emit: vcf
tuple val(meta), path("*.tbi") , emit: tbi
tuple val(meta), path("*stats.txt"), emit: stats
tuple val(meta), path("*.mpileup") , emit: mpileup, optional: true
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def args3 = task.ext.args3 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def mpileup = save_mpileup ? "| tee ${prefix}.mpileup" : ""
"""
echo "${meta.id}" > sample_name.list
bcftools \\
mpileup \\
--fasta-ref $fasta \\
$args \\
$bam \\
$mpileup \\
| bcftools call --output-type v $args2 \\
| bcftools reheader --samples sample_name.list \\
| bcftools view --output-file ${prefix}.vcf.gz --output-type z $args3
tabix -p vcf -f ${prefix}.vcf.gz
bcftools stats ${prefix}.vcf.gz > ${prefix}.bcftools_stats.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
}